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gatk-3.8/public/java/src/org/broadinstitute/sting/commandline
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Eric Banks 14bbba0980 Optimization to method for getting values in ArgumentMatch 
* Very trivial, but I happened to see this code and it drove me nuts so I felt compelled to refactor it.
  * Instead of iterating over keys in map to get the values, just iterate over the values...
 		2013-04-04 23:30:47 -04:00
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Advanced.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
Argument.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ArgumentCollection.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ArgumentDefinition.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ArgumentDefinitionGroup.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ArgumentDefinitions.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ArgumentException.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ArgumentIOType.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ArgumentMatch.java Optimization to method for getting values in ArgumentMatch 2013-04-04 23:30:47 -04:00
ArgumentMatchFileValue.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ArgumentMatchSite.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ArgumentMatchSource.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ArgumentMatchSourceType.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ArgumentMatchStringValue.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ArgumentMatchValue.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ArgumentMatches.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ArgumentSource.java Fixed the logic of the @Output annotation and its interaction with 'required'. 2013-03-14 11:58:51 -04:00
ArgumentTypeDescriptor.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ClassType.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
CommandLineProgram.java Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs) 2013-03-12 10:57:14 -04:00
CommandLineUtils.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
EnumerationArgumentDefault.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
Gather.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
Gatherer.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
Hidden.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
Input.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
IntervalArgumentCollection.java Last manual license update (hopefully) 2013-01-18 16:13:07 -05:00
IntervalBinding.java Intervals: fix bug where we could fail to find the intersection of unsorted/missorted interval lists 2013-04-02 14:01:52 -04:00
MissingArgumentValueException.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
Output.java Fixed the logic of the @Output annotation and its interaction with 'required'. 2013-03-14 11:58:51 -04:00
ParsedArgs.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ParsedListArgs.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ParsingEngine.java Move some VCF/VariantContext methods back to the GATK based on feedback 2013-01-29 16:56:55 -05:00
ParsingEngineArgumentFiles.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ParsingEngineArgumentProvider.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ParsingMethod.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
RodBinding.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
Tags.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
package-info.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00